12mm X rod upgrade issue

I just replaced 10mm X axis rods with the 12mm and LM12 linear bearings. Its bit louder on sliding but very smooth.
No head wobble anymore.

But I have issue with z movement now. At bottom and top positions, steppers seize and either one moves a bit and then get stuck or both are stuck. I checked for squareness with machinist square and it looks alright. No visible misalignment.
I didn’t drill alu endplates as rods went through, but bit tight. I wonder could that cause issues as rest of the frame might not be 100% square and with stiff rods catching on endplates it creates enough resistance for one stepper to skip a step.
Middle part obviously have enough deflection, so Z movement is fine there.

Did anyone had issue with this before?

First, the easy (but not as likely one) - Verify that the x gantry is perpendicular to the Z, there’s enough flex in the rods that you can get away with a crooked X in the middle, but not at the end.

My guess is that the gantry is too narrow or too wide. Loosen the set screws on one side of the rods to very loose. You should be able to get a little bit of movement without too much force. Run the gantry up and down a few times, then tighten the set screws. If it doesn’t move all the way up and down after that, you can start checking squareness of the Z.

Ok, I unscrewed everything and tightened only Xmin side and then went to tighten the other side(with loose set screws on the rods). And i found that threaded rod, printed part is around 2mm from alu bracket)

I mean that would explain pull on the threaded rod. I dont get how was this with 10mm rod as I didnt touch anything else.

Its square enough I suppose. At least it shouldn’t produce that much of a gap.